1.4 Proteins

Question 1

Which monomers make up proteins?

Answer 1

Amino acids.

Question 2

There are … amino acids found in proteins common to all living organisms.

Answer 2

20

Question 3

What is the general structure of an amino acid?

Answer 3

A chiral carbon bonded to:
- an amine group (-NH2) left side
- a carboxylic acid group (-COOH) right side
- a hydrogen atom
- an R group (this is how each amino acid differs → determines its properties)
- central carbon

Question 4

What is the bond between amino acids?

Answer 4

Peptide bond.

Question 5

How is a peptide bond formed?

Answer 5

Peptide bonds are formed when the amine group of one amino acid binds with the carbonyl carbon of another amino acid.
- condensation reaction as a molecule of water is lost (OH from carboxylic group and H from amine group)

Question 6

How is a peptide bond broken?

Answer 6

Hydrolysis reaction (addition of a water molecule).

Question 7

Describe the primary structure of a protein.

Answer 7

The specific order and sequence of amino acids bonded by covalent peptide bonds.
- DNA determines the primary structure
- affects the shape and therefore the function of the protein

Question 8

Describe the secondary structure of a protein.

Answer 8

The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
- bonds can be broken by high temperatures and pH changes

2 shapes:
- α-helix
- β-pleated sheet

Question 9

Describe the tertiary structure of a protein.

Answer 9

Further conformational change of the secondary structure leads to additional bonds forming between the R groups.

3 bonds:
- Hydrogen
- Disulphide
- Ionic

Question 10

What is the role of hydrogen bonds in the structure of proteins.

Answer 10

• form between strongly polar R groups
• weakest
• most common as they form across a wide variety of R groups

Question 11

What is the role of ionic bonds in the structure of proteins.

Answer 11

• form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COOH-) R groups
• stronger than hydrogen bonds but they are not common
• bonds are broken by pH changes

Question 12

What is the role of disulphide bridges in the structure of proteins.

Answer 12

• form between two cysteine R groups
• strongest within a protein, but occur less frequently, and help stabilise the proteins
• can be broken by reduction

Question 13

Describe the quaternary structure of a protein.

Answer 13

proteins that have more than one polypeptide chain

Question 14

Describe the test for a protein.

Answer 14

Biuret Test
1. A few drops of biuret reagent is added
- liquid solution of sample is treated with NaOH or KOH (make it alkaline)
- add a few drops of copper(II) sulfate solution

+VE Result: colour change of blue → purple

Question 15

What are 2 types of proteins?

Answer 15

• globular
• fibrous

Question 16

Describe the structure of haemoglobin.

Answer 16

• it has a quaternary structure four polypeptide chains
• two α–globins and two β–globins
• globular protein
• four haem groups Fe2+
• can bind to four oxygen molecules

Question 17

Describe the structure of collagen.

Answer 17

• three polypeptide chains closely held together by hydrogen bonds to form a triple helix.

Question 18

What are enzymes?

Answer 18

Enzymes are biological catalysts. Structurally, they are globular proteins.

Question 19

What is the lock-and-key model?

Answer 19

• Emil Fisher suggested that both enzymes and substrates were rigid structures that locked into each other very precisely (like a lock and key)
  1. Substrate fits exactly into the complementary active site
  2. This forms an enzyme-substrate complex
  3. Reaction takes place and an enzyme-product complex is formed
  4. Products are released

Question 20

What is the induced-fit model?

Answer 20

• modified model
  1. The substrate does not fit the enzyme’s active site completely
  2. The enzyme and it’s active site can change shape slightly as the substrate molecule enters the enzyme (known as conformational changes) → ensures an ideal binding arrangement between the enzyme and substrate
  3. Forms an enzyme-substrate complex
  4. Reaction takes place and an enzyme-product complex is formed
  5. Products are released

Question 21

How do enzymes work?

Answer 21

Enzymes work by lowering the activation energy of a reaction and in doing so they provide an alternative energy pathway.

Question 22

Describe what is meant by enzyme specificity.

Answer 22

Enzyme active sites have a specific shape (determined by its tertiary structure) that is complementary to specific substrates.
- extremes of heat or pH can change the shape of the active site, preventing substrate binding → denaturation

Question 23

What determines the shape of an enzymes active site?

Answer 23

Its tertiary structure.

Question 24

Name the three types of peptidases and how they act.

Answer 24

• dipeptidases (breaks the peptide bonds in dipeptides to form individual amino acids)
• exopeptidases (breaks a peptide bond at the end of the polypeptide chain)
• endopeptidases (breaks a peptide bond in the middle of the polypeptide chain)

Question 25

Limiting Factors Affecting Enzymes: **Temperature**

Answer 25

- enzymes have a **specific optimum temperature** - **lower temperatures** either **prevent reactions from proceeding** or **slow them down** (low kinetic energy and low frequency of successful collisions) - **high temperatures speed up** the rate of reaction - when temperatures become **too high** the rate of reaction **drops sharply** as the enzyme begins to **denature** (hydrogen bonds break, **change** in **tertiary** structure, **permanently damages the active site** preventing enzyme-substrate complexes from forming)

Question 26

Limiting Factors Affecting Enzymes: **pH**

Answer 26

- all enzymes have an **optimum pH** - enzymes are **denatured** at **extremes of pH** (below and above the optimum pH causes the hydrogen and ionic bonds to break which **alters the shape of the active site**)

Question 27

Limiting Factors Affecting Enzymes: **Enzyme Concentration**

Answer 27

- the **higher the enzyme concentration** in a reaction mixture, the **greater the number of active sites available** and the **greater the likelihood of enzyme-substrate complex formation** - provided there is **sufficient substrate available**, the initial **rate of reaction increases linearly** with enzyme concentration - will not increase rate if **substrate concentration becomes limiting**

Question 28

Limiting Factors Affecting Enzymes: **Substrate Concentration**

Answer 28

- the **greater the substrate concentration**, the **higher the rate of reaction** - as more **successful collisions** and therefore more **kinetic energy**= **higher ROR** - the **likelihood of enzyme-substrate complex formation increases** - will not increase rate when **active site saturation** is reached as the enzyme concentration becomes limiting

Question 29

Limiting Factors Affecting Enzymes: **Inhibitors**

Answer 29

- both types of inhibitors **slow down or stop enzyme activity** - **increasing the concentration of an inhibitor**, therefore, **reduces the rate of reaction** and eventually, if inhibitor concentration continues to be increased, the **reaction will stop completely** - for **competitive** inhibitors, **increasing the substrate concentration can increase the rate of reaction**

Question 30

How does a competitive inhibitor work?

Answer 30

- competitive inhibitors bind to the **same active site** as the complementary substrate as they have a **similar shape**. - this means it’s **competes** with the substrate for the same active site -**occupies the active site**, unbinds as **no reaction occurs** then the complmentary substrate binds

Question 31

How does a non-competitive inhibitor work?

Answer 31

- non-competitive inhibitors bind to the enzyme at an **allosteric site** - this **alters the shape of the active site** - so substrate is **no longer complementary** therefore **prevents the substrate from binding to it** - increasing substrate concentration does **not** increase RoR as active site is no longer complementary

Question 32

Enzymes can be ... (produced and function inside cells) or ... (secreted by cells and catalyse reactions outside cells).

Answer 32

(1) **intracellular** (2) **extracellular**

Question 33

Enzyme reactions can be catabolic meaning ...

Answer 33

they involve the **breakdown of complex molecules into simpler products** (e.g. cellular respiration and hydrolysis)

Question 34

Enzyme reactions can be anabolic meaning ...

Answer 34

they involve the **building up of more complex molecules from simpler ones** (e.g. protein synthesis and condensation)

Question 35

Describe the structure of a protein ( 5 marks)

Answer 35

1. Structure is determined by (relative) position of amino acid/R group/interactions; interactions 2. 3. Primary structure is sequence/order of amino acids; Secondary structure formed by hydrogen bonding (between amino acids); Scout alpha heix B-ploated shoot for sacondary 4. Tertiary structure formed by interactions (between R groups); Accept for 'interactions', hydrogen bonds / disulfide bridges / ionic bonds / hydrophobichydrophilic interactions . Creates active site in enzymes OR Creates complementary/specific shapes in antibodies/carrier proteins/receptor (molecules): 6. Quatemary structure contains >1 polypeptide chain OR Quaternary structure formed by interactions/bonds between polypeptides: Accept for 'intereactions', hydrogen bonds/ disulfide bridges/ionic bonds/hydrophobichydrophilic interactions Accept prosthetic (group)